SIS Converter

If enabled and supported by the corresponding media handler, color settings are transferred from the source file to the SIS file.

If disabled, or enabled and not supported by the corresponding media handler, no special color settings are applied to the SIS file.

The default color settings are as following:

• Color range according to bit depth:
• 8bit: 0 - 255
• 16bit: 0 - 65535
• 32bit float: 0 - 1
• Channel colors according to the number of channels:
• One channel: Gradient from black to white
• Two channels: Channel 1: Gradient from black to red / Channel 2: Gradient from black to green
• Three channels: Channel 1: Gradient from black to red / Channel 2: Gradient from black to green / Channel 3: Gradient from black to blue
• More than three channels: The first three channels are the same as the three channels above. All other channels are the same as one channel.

(OFF by default)

Enable this option, if you don't need blending on the tile borders, for example when you sliced a big image into smaller tiles for easier transfer.

Disabling this option ensures that tiled input files have smooth tile borders after the import is finished.

(ON by default)

If enabled, image data will be compressed without loss of information to reduce the file size.

This is especially useful for environments with limited disk space or transfer bandwidth. The compression rate depends on the image content.

(ON by default)

Enabling this option will create a restore point right after the import process is finished. Using this option enables you to revert any changes to the state after the import and before any changes were made.

Save Folder: This option sets the default folder for any file you wish to import. It is still possible to change the folder on a case by case basis.

Custom Directory: Sets the directory to save the output file in to a folder of your choice.

Source Directory: Sets the directory to save the output file in to the folder of the input file.

The Manual import mapper displays a table with information about what regions of the input files are mapped to what regions in the destination file. Initially, each channel of the input data is specifically mapped to the destination file and will be presented as one line in the mapping table.

For a large number of files, the Manual Mapper approach is not suitable.

The Selection menu provides you with easy-to-use wizards to perform different tasks in order to create custom mappings. Before accessing a specific wizard, please mark all lines inside the mapping table that you want to change. You can press CTRL-A to mark all input files at once.

Sometimes the filenames contain information that define on which dimension each image has to be located in the resulting image.

Sometimes the filenames contain information about channel names.

The Amira-Mesh media handler enables the import of Amira-Mesh files, containing uniform lattice data. Amira-Mesh files can contain different types of data, for instance spatial graphs or stacked lattices. This media handler is not able to read these special data types.

The Amira-Mesh media handler allows you to import images of the following file format: Amira-Mesh (*.am)

The Aperio media handler allows you to import images of the following file format: Aperio (JPEG) (*.svs) , Aperio JPEG2000) (*.svs)

The Metamorph media handler is part of the Bio Media Handler Module which enables the import of some common image formats used in biology-related working areas.

The Metamorph media handler allows you to import images of the following file format: Metamorph (*.stk)

The DeltaVision media handler enables the import of Applied Precision's DeltaVision image files.

The DeltaVision media handler allows you to import images of the following file format: DeltaVision (*.dv)

The Dicom media handler enables arivis SIS Converter to read DICOM containers or DICOMDIR files. These files describe the structure of a DICOM dataset (Digital Imaging and Communications in Medicine) that is most commonly used in medical working areas.

The Dicom media handler allows you to import images in the following file formats: Dicom (*.dcm) , DICOMDIR (*.dicomdir)

The Hamamatsu media handler allows you to import images of the following file format: NDPI (*.ndpi) , Virtual Microscope Specimen (*.vms)

The FreeImage media handler enables the import for most of the common image formats.

It allows you to import images of the following file formats:

• JPEG / JFIF (*.jpg;*.jpeg;*.jif;*.jfif;*.j;*.jpe) TIFF Tagged Image (*.tif;*.tim;*.tiff)
• Windows Bitmap (*.bmp;*.rle;*.vga;*.rl4;*.rl8;*.sys) Portable Network Graphics (*.png)
• CompuServe GIF (*.gif;*.giff)
• JPEG-2000 (*.jp2)
• High Dynamic Range Image (*.hdr)

The ICS media handler allows you to import images of the following file format: ICS 1.0 (*.ics) , ICS 2.0 (*.ids)

The Imaris media handler enables the import of the Bitplane Imaris file format (IMS). The Imaris media handler is using the HDF5 Library.

The Leica media handler enables the import of Leica image file formats.

The Leica media handler allows you to import images of the following file formats: Leica Image File Format (*.lif) , Leica LCS (*.lei)

The LSM media handler enables the import of the LSM file formats.

The Mirax media handler enables the import of the Mirax SlideAC file format. This image format originates from Carl Zeiss Mirax Slide scanner systems and is based on image pyramids.

The Mirax media handler allows you to import images of the following file format: Mirax SlideAC (*.mrxs)

The NIfTI media handler enables the import of the NIfTI (Neuroimaging Informatics Technology Initiative) image file formats.

The NIfTI media handler allows you to import images of the following file formats: single-file(combined data and meta- data)(.nii) ,single-file gzip-compressed (.nii.gz) , dual- file(separate data and meta-data, respectively)(.img/.hdr)

The Nikon media handler enables the import of data created by the Nikon imaging solutions.

The Nikon media handler allows you to import images of the following file format: Nikon ND2 (*.nd2)

The RAWInfo media handler enables the import of raw image files by using a control (*.rawinfo) file that contains dimension information.

The Raw media handler allows you to import images of the following file formats: RawInfo (*.rawinfo)

The Slide Book media handler enables the import of the Slide Book file format.

The Slide Book media handler allows you to import images in the following file format: Slide Book (*.sld)

The VOL media handler enables the import of VG Studio VOL images.

The VOL media handler allows you to import images of the following file format: VOL (*.vol/*.vgi)

To import a VG Studio VOL dataset both files (.vol & .vgi) are needed!

The Zeiss ZVI media handler enables the import of Zeiss image data.

The Zeiss ZVI media handler allows you to import images of the following file formats: Zeiss ZVI (*.zvi) , Zeiss ZISRAW/CZI (*.czi)

• Drag & Drop of folders including several files with the specification of conversion type - multiple input files to be merged or converted independently (1:1)
• Improved handling to avoid unintentional overwriting of image data
• Option to add data as new Image Sets if there is already a target file with the same name
• Define behavior if a target file already exists (Preference option)
• Import of Inspector OBF/MSR data
• Support for the newest LaVision OME format

• Pixel size for multiple image sets using custom import
• CZI import with different pixel types (in one data set)
• Possible problem with Nikon ND2 import for pre-stitched data
• Avoid conversion history corruption
• Small UI glitches
• Separate Start Menu entries for the free and the pro version
• Avoid infinite loop with the same source and destination folders (SIS Converter PRO)
• Improved robustness for unexpected termination

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